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Using the open source platform, the “Spinal Cord Toolbox,” the authors sought to correlate measures of GM, WM, and cross-sectional area pathology on T2 MR imaging with motor disability in 9 patients with acute flaccid myelitis. Proportion of GM metrics at the center axial section significantly correlated with measures of motor impairment upon admission and at 3-month follow-up. The proportion of GM extracted across the full lesion segment significantly correlated with initial motor impairment. This is the first atlas-based study to correlate clinical outcomes with segmented measures of T2 signal abnormality in the spinal cord.